github.com/OpenMS/OpenMS commits | Ecosyste.ms: OpenCollective

[FEATURE] added support for mascot 2.4 to MascotAdapterOnline

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11609 6adb6...

ef997d544b654321501accab39e934cd38b460bd authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed path bug when connecting to a non-standard mascot installation

* i.e., mascot not in http://servername/mascot but http://servername/

git-svn-id: https://open...

52817f02fb31099c1ed23dd449da1d205b1ffb74 authored over 11 years ago by Stephan Aiche <[email protected]>

[TEST] Added class tests for AccurateMassSearchEngine and test data files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11607 6adb6...

729ee5438bb9738c62d2b53f7d7bf34db3e29b27 authored over 11 years ago by Erhan Kenar <[email protected]>

[DOC] multiple documentation fixes (incl. false commit [11604])

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11606 6adb6...

22878bc663b90064b7341142bf8fd0b9314d352c authored over 11 years ago by Stephan Aiche <[email protected]>

[BUILD] minor improvements to mac package building

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11605 6adb6...

d4d93fa80affb396b388654375df6942227bfee3 authored over 11 years ago by Stephan Aiche <[email protected]>

[BUILD] minor improvements to mac package building

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11604 6adb6...

f4d136baffacd8b272b8069d5efd1d93ce1ded75 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX-#586] fix sorting behavior that relies on memory addresses

Instead sort by something stable, here the getOrigin value

git-svn-id: https://open-ms.svn.sour...

ac3accc2d43b583055607c4035d4b466e57645e7 authored over 11 years ago by Hannes Roest <[email protected]>

[DOC] added some documentation on what to do with the release candidate

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11601 6adb6...

e8be2a57d04fd19d9f07d3aeb7e3382ebdd0a39c authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC] added some documentation on what to do with the release candidate

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11600 6adb6...

ec0e7268a0c95bdcfe8f7de615aab91195decb0e authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] Removed MetaboliteSpectralMatcher from release branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11599 6adb6...

2ac580ccab1e1af0e38006ec17a3560f0fa35898 authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX] Removed MetaboliteSpectralMatcher from release branch

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11598 6adb6...

b6799859e33dba8bd627fe738695807170c697fe authored over 11 years ago by Erhan Kenar <[email protected]>

[INTERNAL] moved generation of scan/RT mapping to a function, to allow use in MascotAdapterOnline

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11597 6adb6...

f4cec402d99b535f849b2b18a76017082979d954 authored over 11 years ago by Hendrik Weisser <[email protected]>

[FIX] cleanup (duplicate QApplication)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11596 6adb6...

2c826f46a6a96a4ec5c20412e95638037c9b06fd authored over 11 years ago by Chris Bielow <[email protected]>

[DOC] windows install procedure

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11595 6adb6...

0894ec55142eee7e668475411bfa239aeed66095 authored over 11 years ago by Chris Bielow <[email protected]>

[FEATURE] Add CachedConsumer

The new class allows to consume Spectra/Chromatograms and cache them
directly to disk. It implem...

d8d22554d02057f4e45e21bd8d79df7d16082dbf authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add option to also add cached meta value directly

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11593 6adb6e08-d915-0410-...

0627968125c97833019089e82e660fb5e4d999a2 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] use shared_ptr in SpectrumAccessOpenMS

Previously, a full MSExperiment was transferred to the Handler class and
ownership was not compl...

45bfe3d7cc5b0f41f507a5f1e67aa0c07693f2df authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] allow minimal quality threshold in PeakPicker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11591 6adb6e08-d915-0410-...

e8ff9e25952c87ca51f912f70204252524805ddf authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] bugfix and minor improvements

- bugfix in PeakPickerMRM when dealing with empty chromatograms
- minor improvements in QTCluste...

3b0128d2c0c887dce70338259fd5b9491c202a0c authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] fix MSData consumers

- set default template argument for IMSDataConsumer
- use MSExperiment for MzMLFile::transform
-...

01576c798c1c377057aca7d597edb38e5c234ad7 authored over 11 years ago by Hannes Roest <[email protected]>

[DOC] improve Linux install docu

- explain how to install OpenMS with minimal manually compiled libraries

git-svn-id: https://op...

26be6061e1148a18a84cd76af330e8bca8a67a1b authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] comment out until API is stable

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11587 6adb6...

87a2442791f38d3f06c60e02b8decffe48d6c9fa authored over 11 years ago by Hannes Roest <[email protected]>

[REVERT] Partial revert of r11580

The large sample datasets will be moved to a different repository (for
now)

git-svn-id: https:/...

94f747a3562debb16d30eba67b8eea808542f69e authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] addendum to [11579]

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11585 6adb6e08-d915-0410-...

fb64b9fc07f9bfffa01845b76b181c32107e1271 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] compile with boost < 1.48 possible (fix #582)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11584 6adb6...

ff499b9e99e0b6dbef5ce8274a61fcf610d8c94a authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] Fixed issues with mzTab output in AccurateMassSearch if the input file is a consensusXML

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11582 6adb6...

5cb7680d0a34d3a513ac47ff2287b77ffa64968f authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX] added "xml-stylesheet" to FuzzyDiff whitelist for TOPPAS tests

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11581 6adb...

28302b831753aaf32e534949718ae13631addf99 authored over 11 years ago by Johannes Veit <[email protected]>

[FEATURE-#254] Added TOPPAS pipeline tests (cmake -DENABLE_PIPELINE_TESTING=ON [...]; make test_build; make test)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11580 6adb...

167dd4f257f9fa0e4178bdae8f4a4744c690e071 authored over 11 years ago by Johannes Veit <[email protected]>

[FIX] added template argument to IMSDataConsumer to support all mzml load operations

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11579 6adb6e08-d915-0410-...

8f8d92da61019a8d7030bb5e6645e77ee958e6c5 authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP,BUILD] tutorials now parse the data path from the command line instead of

relying on being in the correct directory. This fixes also problems with CMake's
add_test(WORKING...

6bd83170da28919462e54dd7f65266172add236c authored over 11 years ago by Stephan Aiche <[email protected]>

[DOC,FIX] fixed parameter documentation

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11577 6adb6...

3d1ca56770277f9ac47e8f2fbf725779b4d433a9 authored over 11 years ago by Hendrik Weisser <[email protected]>

[NOP] style fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11576 6adb6...

0c174a4be3c006ce1128b1d0960566158e11df94 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[FIX] Fixed a huge bug that resulted in no consensusXML input support for the AccurateMassSearch util (hrhrhr ;-)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11575 6adb6...

42f2063e88f6d699bc6493d2248b557dd7d1875e authored over 11 years ago by Erhan Kenar <[email protected]>

[BUILD] pyOpenMS: print Cython version number, no hex-chars in code

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11574 6adb6...

cb67de6be50ddaed4f7e4f16dcdbb33a1913d35b authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] addendum to [11567], fixed handling of item lists

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11573 6adb6...

fc5ce40ecedf1d88a6442ad7465c8a796dccd87f authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] addendum to [11567], fixed test files

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11572 6adb6...

3621eacd12a5fbbd01984457f45b44178fa8bf68 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] Added a switch for an alternative trace extension method (trace_termination_criterion)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11571 6adb6...

a59ce2c29e2147845dbafba07fb3c4a647f3ba65 authored over 11 years ago by Erhan Kenar <[email protected]>

updated documentation for XTandemAdapter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11570 6adb6...

b7115fab6be9ee0a12044c90edcbd480c22d8323 authored over 11 years ago by Mathias Walzer <[email protected]>

[FIX] Added a switch for an alternative trace extension method (trace_termination_criterion)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11569 6adb6...

1facf4335a8c377868ca4299c3563e0cef705c73 authored over 11 years ago by Erhan Kenar <[email protected]>

[FEATURE,FIX] added support for CTD 0.3 Schema to TOPPBase's writeCTD method

* all CTDs exported by prepare_knime_package validate against the new schema

git-svn-id: https...

a7a997899474126f04766e7c11f65ff4babc6a72 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX,FEATURE] updated ParamXMLHandler/File to the new 1.6.2 schema

* includes tests
* is backward compatible to pre1.6.2 param files

git-svn-id: https://open-ms...

906c632d7387c12a1af4ef4d89a5ac1eda3e23c1 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX,NOP] fixed some bugs in the Param 1.6.2 schema

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11566 6adb6...

588b36b54bfef0d42ec63fddbb26e35736a9ddc7 authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] fixed version handling in ParamXMLHandler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11565 6adb6...

4a3fbe1e109b4af9f39ed757371c2a3a169e26de authored over 11 years ago by Stephan Aiche <[email protected]>

removed unused handlerfile for qcml

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11563 6adb6...

dc0ed301fadbff00030780748bfd2a2cdd4478a4 authored over 11 years ago by Mathias Walzer <[email protected]>

[DOC,INTERNAL] added some additional information on parameter documentation in internal FAQ

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11562 6adb6...

eb7a15a5ab4948b76eeb414b7c8ce5b75a7a999d authored over 11 years ago by Timo Sachsenberg <[email protected]>

[NOP,STYLE] cpplint style fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11561 6adb6...

9fd690ab8ca8fa92303497ad2a33770a8553ceeb authored over 11 years ago by Timo Sachsenberg <[email protected]>

[STYLE] fix test after r11559

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11560 6adb6...

51047f65ae2de2c6eb7d3c57e6ca69adff3318a3 authored over 11 years ago by Hannes Roest <[email protected]>

[NOP,STYLE] cpplint style fixes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11559 6adb6...

dfa6069af14d02c41c1a2b7d1611c407b2cc12d6 authored over 11 years ago by Timo Sachsenberg <[email protected]>

[DOC, NOP] improved on the documentation of PeakPickerRapid, RNPxl and RNPxlXICFilter

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11558 6adb6...

3f936233504ef2d54aa1a6b1f2edc481ee93c555 authored over 11 years ago by Timo Sachsenberg <[email protected]>

Revert "[FIX] Fixed bug in FeatureFinderMetabo that could cause negative feature intensities"

This reverts commit r11549.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/bra...

512f95984c16e40b1018b59008541c560ac01e6d authored over 11 years ago by Hannes Roest <[email protected]>

Revert "[FIX] Added check for 0.0 intensity peaks (common in Orbitrap/FT spectra); set window size of median noise estimator to 50 Da"

This reverts commit r11547.

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/bra...

d446655ede2c1130d4c0bf2256b875c2e5df6f71 authored over 11 years ago by Hannes Roest <[email protected]>

revert commit

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11554 6adb6e08-d915-0410-...

9be264739d97c9257a9bef186bde29d07f7b5194 authored over 11 years ago by Christian <[email protected]>

[GSL Removal] wrapped all gsl functions

All gsl functions are moved to MATH/gsl_wrapper and all gsl includes are replaced by the wrapper...

39cbb9b2bb9bc4f0237cb016c8010cab046cc25c authored over 11 years ago by Christian <[email protected]>

[DOC] clarification: ordered data structure required (cf. r11544)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11552 6adb6...

ce80a578d148c1c77aa16d5926c626187e154b18 authored over 11 years ago by Hendrik Weisser <[email protected]>

[NOP,FIX] fixed a couple of checker errors

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11551 6adb6...

f62c9db9392205f970a01da8e78d36b5cc874626 authored over 11 years ago by Stephan Aiche <[email protected]>

[BUILD] makes calling make doc/doc_tutorials manually is now obsolete

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11550 6adb6...

f0325c081f64d20d4ef024d02eea1d1ab91bc28e authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] Fixed bug in FeatureFinderMetabo that could cause negative feature intensities

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11549 6adb6...

21c9cb9094d843315908a30624a4684cf5e8ac55 authored over 11 years ago by Erhan Kenar <[email protected]>

[DOC] updated documentation

- updated linux build instructions with PyOpenMS (and type fixes)
- updated mac build instructio...

ce14c3494c7f1a5e21e1e65d572e1fa94bf32ca0 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] Added check for 0.0 intensity peaks (common in Orbitrap/FT spectra); set window size of median noise estimator to 50 Da

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11547 6adb6...

cb13335d5ffd47354bc0f2e9cb545ab8746e815f authored over 11 years ago by Erhan Kenar <[email protected]>

[FIX] added QCExtractor to ToolHandler

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11546 6adb6...

055ff322792ea08e321ee1251405b1553dd7da55 authored over 11 years ago by Stephan Aiche <[email protected]>

[TEST] test for bug #570 (ordering of neighbor distances)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11545 6adb6...

a363849a0a1457db4670adff6d69e60c5d40add6 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#570] bugfix (ordering of neighbor distances)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11544 6adb6...

7d95a3b747fb47473b5a3ad74c5383660650976c authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] write warning regarding Issue #420

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11542 6adb6...

bd798e9432186824c0071b4622125e848f8173f2 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#289] partial fix for #289, throw NotImplemented

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11541 6adb6...

2c0756b42e39d16d23d4d83f2c3b2d0bf0e637db authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#569] fix multiple QApplication instances

QApplication should be a singleton, fix this

git-svn-id: https://open-ms.svn.sourceforge.net/sv...

acf78e07625403acc4d9844654fc40f4004d8076 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#184, TEST] ConsensusFeature does not inherit from std::set anymore. API augmented with minimal set of STL-equivalents.

* Tests adapted accordingly

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/bra...

4e20e1bb4ad5794c2f6d1fef9b24c0b55713b0d7 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] using unused variable (and fixing a compile error on VS2013 at the same time)

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11538 6adb6...

209288a0a0c465f4678f5ea2b8371bc6b0301263 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] warning

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11537 6adb6...

076208ef6afb59c876ccfd2b8f370bbd53a18238 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] compile error

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11536 6adb6...

5cda262c3341c49784e712a66df73dd06e86a8eb authored over 11 years ago by Chris Bielow <[email protected]>

[DOC, BUILD] * fix tutorial testing CWD

* remove obsolete "tutorial" target (cant be executed platform independent and is basically the ...

25855f339cbe7423f54f12e433348e1ba908d628 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] VS2013 compatibility: added missing includes and removed/changed operators

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11534 6adb6...

798e9bb047c974597fcfe4cfcf3a953b2d88e8e6 authored over 11 years ago by Chris Bielow <[email protected]>

[FIX] fix tool name

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11533 6adb6...

723ffc585888118fa2a9e81500317e5451d9dc89 authored over 11 years ago by Hannes Roest <[email protected]>

[BUILD] integrate the two implementations into the build system

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11532 6adb6e08-d915-0410-...

ab974df2ea089b9f5a1f73e6b3b6564151a8f15b authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] fix previous commit

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11531 6adb6e08-d915-0410-...

92a1f1e66d85ac4a9bfe788379042675414a39c8 authored over 11 years ago by Hannes Roest <[email protected]>

[TEST] add test for LowMemPeakPickerHiRes

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11530 6adb6e08-d915-0410-...

9f9d1a8140d6ebdce726855c9399ef46dc4cc2f0 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE-#564] add LowMemory PeakPicker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11529 6adb6e08-d915-0410-...

f79175b7038ff0d0cad251c3015722e2e344a48b authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE-#564] add two sample Implementations for DataAccess

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11528 6adb6e08-d915-0410-...

be5c3b0457542b91624bb4fa8eddec1512d7aafe authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE-#564] add consumer to MzMLFile

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11527 6adb6e08-d915-0410-...

4cb4ccf685101d52b35b46a12312de821c983465 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add Interface for data consumer

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11526 6adb6e08-d915-0410-...

b6ce878aa20130a99df0d93578fef7218b4db815 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add option to estimate size of MzMLFile

- using loadSize it is not possible to estimate the file size

git-svn-id: https://open-ms.svn.s...

efba72e8ea2e603fea0bac35645a35be6ebf3b58 authored over 11 years ago by Hannes Roest <[email protected]>

[BUILD] better message about Python interpreter

more informative message about which Python interpreter will be used for
building pyOpenMS and h...

4b3dade80ba54f3c5a5bb842cdf854921d10709d authored over 11 years ago by Hannes Roest <[email protected]>

[FIX,TEST] fix tests after refactoring

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11523 6adb6e08-d915-0410-...

6efb519efec64576dd0e3692d158c2f22b54a4d3 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX-#565,TEST] fixed writing variable modifications to xtandeminput file

* modifications were written as mass@N-term but should be written as mass@[
* adopted XTandemI...

66e86cabcb63523a01507317bc1423a08377454c authored over 11 years ago by Stephan Aiche <[email protected]>

[FIX] after refactoring

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11521 6adb6e08-d915-0410-...

08422c305d843c0a75f3ef0ece50878d04c7b8f3 authored over 11 years ago by Hannes Roest <[email protected]>

added CTD and updated Param schema

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11520 6adb6...

8a1f69b0df0742204b8b9bbdbe4bf9056bd7e574 authored over 11 years ago by Mathias Walzer <[email protected]>

[FEATURE] add two new library scores to OpenSwath

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11517 6adb6e08-d915-0410-...

c26ab991be416d88acbd59c37d7fe7b348f97bf3 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] refactoring: split up the three unrelated scores into different functions

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11516 6adb6e08-d915-0410-...

e424dc079d0dbfec8edf33d9bc7201d97fa89588 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] fix compiler warnings

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11515 6adb6e08-d915-0410-...

300573aa437c3c281ff7ad2a5c705aecffdf1731 authored over 11 years ago by Hannes Roest <[email protected]>

[BUILD] fixed execution error of Tutorial tests when build with MSVC

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11514 6adb...

f96419ff6607730eb91de05074e31db206ec4590 authored over 11 years ago by Stephan Aiche <[email protected]>

[NOP] removed unused inlcudes in FFPicked algo

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/branches/Release1.11@11513 6adb6...

9188c7b466e0a0b3572f6b2e869b2f9e62c50fab authored over 11 years ago by Stephan Aiche <[email protected]>

DOC for params

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11510 6adb6e08-d915-0410-...

c29e8385c145bc272baa63774edef97db612e38b authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add the MRMTransitionGroupPicker TOPP tool

[TEST] add test for MRMTransitionGroupPicker

git-svn-id: https://open-ms.svn.sourceforge.net/sv...

ca8bcb4394cd5cf1beebc0688fd07c24add51659 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] add method to compute peak quality to MRMTransitionGroupPicker

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11508 6adb6e08-d915-0410-...

387e2d10f10f6adadd3570f268d3d56a5a8da6e0 authored over 11 years ago by Hannes Roest <[email protected]>

[FIX] fix peak calculation in MRM PeakPicking

- adapt peak calculation to how PeakPickerHiRes defines the peak. This
assumes that at least 3...

fae53def6a4afb8d15dc07522dc5635dcdc57ef9 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] PeakPickerMRM add new picking method

- add "corrected" method which uses the smoothed chromatogram to pick
- ignore peak width when l...

9dbd980a21d0256511d38b8e8b5ee734633eced5 authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] allow Crawdad peak picking in OpenMS using PeakPickerMRM

- if OpenMS was compiled with Crawdad support, this option can be chosen
for MRM peak picking
...

8cc1ab11f03a43a00c1a10920e3ffaf327a6003f authored over 11 years ago by Hannes Roest <[email protected]>

[BUILD] allow build system to compile with crawdad

Crawdad is a chromatographic peak picker from the MacCoss lab. This
patch allows to link OpenMS ...

1e2d0f84b2762caa8402d228811ace4789425261 authored over 11 years ago by Hannes Roest <[email protected]>

[INTERNAL] remove smoothed chromatogram from interface of PeakPickerMRM

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11503 6adb6e08-d915-0410-...

1b364c13c5dfdd308987a55c274686e14c566e03 authored over 11 years ago by Hannes Roest <[email protected]>

[TEST] add test for PeakPickerMRM

add to test

git-svn-id: https://open-ms.svn.sourceforge.net/svnroot/open-ms/OpenMS@11502 6adb6e...

bdf93b13b16c55e563a147209157791257eb18fa authored over 11 years ago by Hannes Roest <[email protected]>

[FEATURE] do consistency check in MRMTransitionGroupPicker

check that the right and left borders of all peaks found are consistent
(to notice shoulders and...

60039343f84a37b6331373cf32021d1e9ae1b21f authored over 11 years ago by Hannes Roest <[email protected]>